• 3 days.

  • 1 day of lectures and roundtables.

  • 2 days of hands-on practicals.

  • April 12-14, 2021.

  • At no cost.

  • Virtual workshop

This workshop will be held remotely, registration is required, and all times are ET.

The registration deadline has passed.

Questions? Email nccatinfo [at] nysbc.org.


NCCAT Tomography Short Course

April 12-14, 2021

SEMC and NCCAT will be offering a 3-day workshop focused on the theory and practice of tomographic methods. Cryoelectron tomography (cryoET) is a powerful new method for directly visualizing macromolecular associations and organization in native cells Traditionally, macromolecular structure determination has been limited to the analysis of isolated molecules and structures. CryoET has the unique ability to visualize macromolecular organization in native cells; it utilizes the intrinsic contrast of frozen cellular material to directly image macromolecules.

[instructor bios][recording playlist]

Short Course Agenda

April 12, 2021
Day 1: Lectures and Roundtables

recordings: [Day 1 first half][Day 2 second half]

12:00-12:05 Welcome
12:05-12:50 Lecture 1 – Intro and overview of ET
Wei Dai (Rutgers University)  [pdf of slides]
12:50-13:35 Lecture 2 – FIB-SEM
Bill Rice (New York University)  [pdf of slides]
13:35-14:20 Roundtable 1 – Making windows into cells & Choosing the right in situ target and model system
14:20-14:45 Break
14:45-15:30 Lecture 3 – Cryo-Applications and sub-tomogram averaging
Alex Noble (NYSBC/SEMC)  [pdf of slides]
15:30-16:15 Lecture 4 – Automated reconstruction, subtomogram averaging methods & data interpretation
Steven Ludtke (Baylor College of Medicine)  [pdf of slides]
16:15-17:00 Roundtable 2 – The future of in situ cellular structural biology
17:00-17:30 Closing and networking/break out rooms

April 13, 2021
Day 2: Practical – Appion Protomo (
limited space available)

11:00-11:45 Practical pre-requisite – Computational setup for workshop [AWS startup pdf]
11:45-12:00 Break
12:00-12:05 Welcome
12:05-13:00 Roundtable 3 – Introductions and flash talks by short course attendees
[Flash talk speaker list][Flash talk slide deck pdf] recording: [Flash talks]
13:00-17:00 Practical 1
Appion III : Fiducial-less Tomography Practical
Alex Noble (NYSBC/SEMC)
[tutorial information]  recording: [Appion-protomo & Dynamo]
13:00-13:30 Full Overview – Tilt-Series Collection, Appion-Protomo alignment, and Sub-tomogram Processing
13:30-14:00 In-Depth Appion-Protomo Workflow
14:00-14:30 Q&A and Practice!
14:30-15:00 Discussion/Break
15:00-15:10 Overview – Sub-Tomogram Alignment and Dynamo
15:10-15:35 Particle Picking using a Template
15:35-16:00 Membrane, and Filament Picking
16:00-16:30 Sub-Tomogram Alignment, Classification, and tools to transfer to Warp/M/Relion
16:30-17:00 Q&A and Practice!
17:00 End

April 14, 2021
Day 3: Practical – EMAN2
(limited space available)

11:00-11:45 Practical pre-requisite – Computational setup for workshop [AWS startup pdf]
11:45-12:00 Break
12:00-12:05 Welcome
12:05-16:45 Practical 2
EMAN2 tools, sub-tomogram averaging and annotation
Muyuan Chen (Baylor College of Medicine)
[tutorial information]  recording: [EMAN2]
12:05-12:50 Basic user interface and visualization of raw data.
12:50-13:35 Tilt series alignment, tomogram reconstruction and CTF estimation
13:35-14:30 Methods for picking particles from tomograms
14:30-15:00 Break
15:00-16:15 Generating initial model and setting up subtomogram averaging runs
16:15-16:45 Q&A
16:45-17:00 Closing & Wrap up

*All times ET.


Rutgers University

Wei Dai

Baylor College of Medicine

Steven Ludtke

New York University

William Rice

New York Structural Biology Center

Alex Noble

Baylor College of Medicine

Muyuan Chen